The economies of scale provided by large genome-sequencing service centers make outsourcing significantly more cost effective than in-house sequencing for most academic researchers. But these buyers, whose work relies on fast turnaround and extremely accurate data, need to beware. Not all sequencing providers are alike.

That was the message delivered last week by the New York Genome Center’s Senior Vice President of Informatics, Dirk Evers, and Herbert Auer, director of the Functional Genomics Core at the Institute for Research in Biomedicine of the Parc Cientific de Barcelona. The men gave back-to-back presentations at the 2012 Bio-IT World Europe Conference and Expo in Vienna, Austria.

Auer, who runs what he calls a “virtual genomics center” without in-house sequencing machines, said he and his colleagues decided to outsource when they realized the costs for running a machine are so great that “you either sequence 1,000 samples per year or you burn money.” Instead, they prepare their DNA samples for sequencing but ship them to one of five commercial providers for processing. Auer pointed to the nascent New York Genome Center as a possible future provider.

“Financially it makes more sense at scale,” Evers agreed. He said the New York Genome Center’s 11 institutional founding members are already benefiting from outsourcing to the center. New York is “a very large [biosciences] hub that did not have sufficient sequencing resources,” Evers said.

The city's medical centers alone see 1.2 million hospital admissions annually, he noted -- a figure that does not include admissions at the 15 hospitals and medical centers of NYGC-member North Shore-LIJ Health System. What’s more, the New York City region is the nation’s top employer of life scientists and second largest recipient of National Institutes of Health funding.

In order to meet the growing need for DNA analysis in New York and beyond, Evers said the New York Genome Center aims to be one of the largest genetics and genomics facilities in North America. It will offer sequencing, high-performance computing, and bioinformatics services from a seven-floor headquarters in lower Manhattan.

Institutional members will be able to pool resources to create efficiencies they couldn’t achieve on their own. Already, with operations in a pilot phase in rented space at the Rockefeller University, Evers said members “are saving money just because we have deals with the large vendors.”

By working with a variety of large-scale sequencing providers, however, Auer’s team in Barcelona has found that not all provide the same quality nor can all conform to academic users’ needs. For example, they tend to want DNA samples so big that “my researchers fall dead off their chair” when they hear the amount, Auer joked. Some providers are not able to alter their processes to do something out of the ordinary, and the turnaround can be too slow for the competitive academic environment. Even more troublesome, some provide inadequate documentation of how the samples were processed. “When you’re concerned about data quality, this can be a serious, serious issue,” Auer said.

Evers agreed that quality is crucial. “We’re trying to achieve the standard that [Auer] would like to see,” he said. NYGC’s business model is designed to take advantage of its scale to keep costs down while offering state-of-the-art services, he said. For example, the center is prepared to replace its sequencing instrument fleet every three years to keep pace with rapid advances in technology. Data processing and storage choices are similarly flexible, ranging from in-house capacity at headquarters to secure off-site and cloud services. “If you asked me which technology is going to win in two years, at this point in time I wouldn't risk answering that question,” Evers said. “I want to be able to react and choose the most cost-efficient and safest choice.”

In addition to bleeding-edge genome sequencing technologies and services, NYGC will offer custom data analysis. Member institutions will benefit from a bioinformatics department—projected to be 45 strong by the end of 2013—instead of bulking up their own in-house bioinformatics expertise. This is “the real promise,” Evers said: “a large resource of experts who can actually analyze and interpret the data.”

Chelsea Wald is a freelance science writer and editor in Vienna, Austria. She has written for Science and New Scientist, among others.